OGC                     Optimal genetic contribution
add.array               Add a genotyping array
add.combi               Add a trait as a linear combination of other
                        traits
add.diag                Add something to the diagonal
add.diversity           Add additional diverse material to a population
add.fixed.effects       Add fixed effects to traits
add.founder.kinship     Add a relationship matrix for founder
                        individuals
alpha_to_beta           Moore-Penrose-Transfomration
analyze.bv              Analyze genomic values
analyze.population      Analyze allele frequency of a single marker
bit.snps                Decoding of bitwise-storing in R
bit.storing             Bitwise-storing in R
breeding.diploid        Breeding function
breeding.intern         Internal function to simulate one meiosis
breeding.intern1        Internal function to simulate one meiosis
breeding.intern2        Internal function to simulate one meiosis
breeding.intern3        Internal function to simulate one meiosis
breeding.intern4        Internal function to simulate one meiosis
breeding.intern5        Internal function to simulate one meiosis
breeding.intern6        Internal function to simulate one meiosis
breeding.intern7        Internal function to simulate one meiosis
breeding.intern8        Internal function to simulate one meiosis
bv.development          Development of genetic/breeding value
bv.development.box      Development of genetic/breeding value using a
                        boxplot
bv.standardization      BV standardization
calculate.bv            Calculate breeding values
cattle_chip             Cattle chip
check.parents           Relatedness check between two individuals
chicken_chip            chicken chip
clean.up                Clean-up recombination points
codeOriginsR            Origins-coding(R)
combine.traits          Combine traits
computing.costs         Compute costs of a breeding program
computing.costs.cohorts
                        Compute costs of a breeding program by cohorts
computing.snps          Compute genotype/haplotype
computing.snps_single   Compute genotype/haplotype in gene editing
                        application
creating.diploid        Generation of the starting population
creating.phenotypic.transform
                        Create a phenotypic transformation
creating.trait          Generation of genomic traits
decodeOriginsR          Origins-Decoding(R)
demiraculix             Remove miraculix-coding for genotypes
derive.loop.elements    Derive loop elements
diag.mobps              Diagonal matrix
edges.fromto            Detection of parental/child nodes
edit_animal             Internal gene editing function
effect.estimate.add     Estimation of marker effects
effective.size          Estimate effective population size
epi                     Martini-Test function
ex_json                 ex_json
ex_pop                  ex_pop
exist.cohort            Function to extract if a cohort exists
find.chromo             Position detection (chromosome)
find.snpbefore          Position detection (SNPs)
founder.simulation      Founder simulation
generation.individual   Function to generate a new individual
get.admixture           Admixture Plot
get.age.point           Derive age point
get.allele.freq         Calculate allele frequencies
get.bv                  Export underlying true breeding values
get.bve                 Export estimated breeding values
get.class               Derive class
get.cohorts             Export Cohort-names
get.cohorts.individual
                        Derive ID on an individual
get.computing.time      Derive computing time
get.creating.type       Derive creating type
get.culling.time        Derive culling time
get.culling.type        Derive culling type
get.cullingtime         Derive time of culling
get.database            gen/database/cohorts conversion
get.death.point         Derive death point
get.dendrogram          Dendrogram
get.dendrogram.heatmap
                        Dendrogram Heatmap
get.dendrogram.trait    Dendrogram
get.distance            Calculate Nei distance between two or more
                        population
get.effect.freq         Compute marker frequency in QTL-markers
get.effective.size      Estimate effective population size
get.fixed.effects.p     Export parametrization of fixed effects
get.geno                Derive genotypes of selected individuals
get.geno.time           Derive genotyping timepoint
get.genotyped           Derive genotyping status
get.genotyped.snp       Derive which markers are genotyped of selected
                        individuals
get.haplo               Derive haplotypes of selected individuals
get.id                  Derive ID on an individual
get.index               Putting together indices for GxE / multi trait
get.infos               Extract bv/pheno/geno of selected individuals
get.is.first            First copy
get.is.last             Last copy
get.litter              Export litter
get.litter.effect       Export litter effect
get.maf                 Calculate minor allele frequencies
get.map                 Map generation
get.ngen                Number of generations
get.nindi               Number of individuals
get.npheno              Export underlying number of observations per
                        phenotype
get.ntrait              Number of traits
get.pca                 Principle components analysis
get.pedigree            Derive pedigree
get.pedigree.visual     Draw pedigree
get.pedigree2           Derive pedigree including grandparents
get.pedigree3           Derive pedigree parents and grandparents
get.pedigree_old        Derive pedigree
get.pedmap              Generate plink-file (pedmap)
get.pen                 Export pen ID
get.pen.effect          Export pen-effects
get.pheno               Export underlying phenotypes
get.pheno.off           Export underlying offspring phenotypes
get.pheno.off.count     Export underlying number of used offspring for
                        offspring phenotypes
get.pheno.single        Export underlying phenotypes
get.pheno.time          Derive phenotyping time point
get.phylogenetic.tree   Phylogenetic Tree
get.plink               Generate binary plink-file
get.pool                Export founder pool
get.pool.founder        Derive founder pool
get.qtl                 QTL extraction
get.qtl.effects         QTL effect extraction
get.qtl.variance        QTL effect variance extraction
get.recombi             Derive genetic origins
get.reliability         Export underlying reliabilities
get.selectionbve        Export derived breeding values based on the
                        selection index
get.selectionindex      Export underlying last used selection index
get.sex                 Extraction of individual sex
get.size                Number of individuals in each generation
get.snapshot            Derive snapshot of selected individuals
get.snapshot.single     Derive snapshot of selected individuals
get.time.point          Derive time point of generation
get.trafo.p             Export parametrization of fixed effects
get.trafo.p.single      Export parametrization of fixed effects
get.trait.name          Name of traits
get.uhat                Export estimated SNP effects
get.variance            Derive variances components (add/dom)
get.variance.components
                        Derive variance components
get.vcf                 Generate vcf-file
group.diff              Exclude individuals from a database
inbreeding.emp          Empirical kinship
inbreeding.exp          Expected inbreeding
insert.bv               Manually enter breeding values
insert.bve              Manually enter estimated breeding values
insert.pheno            Manually enter phenotypes
insert.pheno.single     Manually enter phenotypes
json.simulation         Simulation of a breeding program based on a
                        JSON-file from MoBPSweb
kinship.development     Development of genetic/breeding value
kinship.emp             Empirical kinship
kinship.emp.fast        Approximate empirical kinship
kinship.emp.fast.between
                        Approximate empirical kinship
kinship.exp             Derive expected kinship
ld.decay                Generate LD plot
maize_chip              maize chip
matrix.posdef           Projection positive definite
merging.cohorts         Merging of cohorts
merging.trait           Generation of genomic traits
miesenberger.index      Miesenberger Index
miraculix               Add miraculix-coding for genotypes
mutation.intro          Mutation intro
new.base.generation     Set new base generation
ogc.mobps               Breeding function
optimize.cores          Optimize generation cores
pedigree.matrix         Derive pedigree relationship matrix
pedigree.simulation     Simulation of a given pedigree
pedmap.to.phasedbeaglevcf
                        Internal function to perform imputing/phasing
pig_chip                pig chip
plot.population         Plot Population
recalculate.bv          Recalculate genomic values
recalculate.manual      Recalculate genomic values
recombination.function.haldane
                        Haldane recombination function
renaming.cohort         Rename a cohort
rowMedian               Row-wise Median
scaling.relationship    scaling.relationship
set.age.point           Set age points
set.class               Set class
set.default             Set defaults
set.mean.pool           Set differences between founder pool
set.time.point          Set time point
sheep_chip              sheep chip
sortd                   Apply sort and unique
ssGBLUP                 Single Step GBLUP
summary.population      Summary Population
vlist                   Generation of a sublist
write.pedigree          write.pedigree.mixblup
